utils

freeart.utils

Python utils for freeart.

freeart.utils.reconstrutils: some utils linked to the reconstruction

group some functions used for reconstruction

freeart.utils.reconstrutils.decreaseMatSize(mat)

will decrease the matrice size if possible where one dimension has only one element

freeart.utils.reconstrutils.increaseMatSize(mat, firstPos)

Simple function which will add a dimension to the current matrice

Parameters:

• mat – the matrice for which we want to remove a dimension
• firstPos – if true remove the first position else remove the last

freeart.utils.reconstrutils.savePhantom(data, fileName, overwrite=False)

will create an edf file to store the given data

Parameters:

• data – the data to save
• fileName – the localisation to know where to save the data

freeart.utils.reconstrutils.LoadEdf_2D(fName, frame=0)

Load data from the given edf file

Parameters:

• fName – the name of the file
• frame – if multiple frame file, will use theis parameter to load a specific frame

freeart.utils.reconstrutils.makeFreeARTFluoSinogram(phantom, absMat, selfAbsMat, numAngle, detSetup, oversampling, beamCalcMeth, outRayPtCalcMeth, minAngle=0.0, maxAngle=6.283185307179586, subdivisionValue=3, turnOffSolidAngle=False, I0=1.0, voxelSize=1.0)

Generate the fluorescence sinogram

Parameters:

• phantom – The initial phantom (density * probability of emission of photon…)
• absMat – absorption of the incoming. Aka \({\mu}_{E_0}{\rho}x\)

Returns:

• sinogram (numpy array of float64 )
• angles list of angles of projection

Warning

all angle values must be given in rad

freeart.utils.reconstrutils.convertToFisxMaterial(materialName, material)

convert a material defined in a dictionnary (from tomoGUI for example. Used to be saved and loaded ) in a fisx Material. Won’t do the registration

Parameters:

• materialName – the name to attribute to the fisx material
• material – the material defined in a dictionary

Returns:

the fisx material

initial material structure looks like : materialName = “My_mat” material = {‘Comment’:”No comment”,

‘CompoundList’:[‘Cr’, ‘Fe’, ‘Ni’], ‘CompoundFraction’:[18.37, 69.28, 12.35], ‘Density’:1.0, ‘Thickness’:1.0}

Final structure is a fisx Material : steel = {“Cr”:18.37,

“Fe”:69.28, # calculated by subtracting the sum of all other elements “Ni”:12.35 }

material = Material(“My_mat”, 1.0, 1.0) material.setComposition(steel)

freeart.utils.genph: phantom generator

class freeart.utils.genph.PhantomGenerator

Bases: object

Class for generating different Phantoms

get3DPhantomSheppLogan(n)

Parameters:n – The width (and height) of the phantom to generate Returns:A numpy array of dimension n*n fit with the sheppLogan phantom

get2DPhantomSheppLogan(n, ellipsoidID=None)

Parameters:

• n – The width (and height) of the phantom to generate
• ellipsoidID – The Id of the ellipsoid to pick. If None will produce all the ellipsoid

get2DPhantomMetal(n, ellipsoidID=None)

Parameters:

• n – The width (and height) of the phantom to generate
• ellipsoidID – The Id of the ellipsoid to pick. If None will produce all the ellipsoid

freeart.utils.benchmark: tool for benchmarking

Benchmark file.

freeart.utils.benchmark.benchmark_tx_projection(oversamplings, widthsToTest, nbAngle)

Create a graph for benchmarking the transmission forward projector

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test

freeart.utils.benchmark.benchmark_tx_reconstruction(oversamplings, widthsToTest, nbAngle, nbIter)

Create a graph for benchmarking the transmission reconstructor

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test
• nbIter – the number of iteration to test (one iteration launch nbAngle back projection)

freeart.utils.benchmark.benchmark_fluo_projection(oversamplings, widthsToTest, nbAngle, outgoingraypointsmethods)

Benchmark the fluo projection

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test
• outgoingraypointsmethods – the list of outgoingrayalgorithm to test

freeart.utils.benchmark.benchmark_fluo_reconstruction(oversamplings, widthsToTest, nbAngle, outgoingraypointsmethods, nbIter)

benchmark the fluo reconstruction

Parameters:

• oversamplings – the list of oversamplings to test
• widthsToTest – the list of phantom width to test
• nbAngle – the number of projection to test
• outgoingraypointsmethods – the list of outgoingrayalgorithm to test
• nbIter – the number of iteration to test (one iteration launch nbAngle back projection)